[2024-01-25 17:51:50,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:50,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:50,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgf286f622-2f74-4e8a-8006-39212aa7d0ce/dqc_reference
[2024-01-25 17:51:51,930] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:51,930] [INFO] Task started: Prodigal
[2024-01-25 17:51:51,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg687f3fbb-0903-450d-a213-640eccdec944/GCF_021864535.1_ASM2186453v1_genomic.fna.gz | prodigal -d GCF_021864535.1_ASM2186453v1_genomic.fna/cds.fna -a GCF_021864535.1_ASM2186453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:05,117] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:05,117] [INFO] Task started: HMMsearch
[2024-01-25 17:52:05,117] [INFO] Running command: hmmsearch --tblout GCF_021864535.1_ASM2186453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf286f622-2f74-4e8a-8006-39212aa7d0ce/dqc_reference/reference_markers.hmm GCF_021864535.1_ASM2186453v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:05,381] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:05,382] [INFO] Found 6/6 markers.
[2024-01-25 17:52:05,424] [INFO] Query marker FASTA was written to GCF_021864535.1_ASM2186453v1_genomic.fna/markers.fasta
[2024-01-25 17:52:05,424] [INFO] Task started: Blastn
[2024-01-25 17:52:05,424] [INFO] Running command: blastn -query GCF_021864535.1_ASM2186453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf286f622-2f74-4e8a-8006-39212aa7d0ce/dqc_reference/reference_markers.fasta -out GCF_021864535.1_ASM2186453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:06,335] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:06,338] [INFO] Selected 12 target genomes.
[2024-01-25 17:52:06,338] [INFO] Target genome list was writen to GCF_021864535.1_ASM2186453v1_genomic.fna/target_genomes.txt
[2024-01-25 17:52:06,345] [INFO] Task started: fastANI
[2024-01-25 17:52:06,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg687f3fbb-0903-450d-a213-640eccdec944/GCF_021864535.1_ASM2186453v1_genomic.fna.gz --refList GCF_021864535.1_ASM2186453v1_genomic.fna/target_genomes.txt --output GCF_021864535.1_ASM2186453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:17,842] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:17,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf286f622-2f74-4e8a-8006-39212aa7d0ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:17,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf286f622-2f74-4e8a-8006-39212aa7d0ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:17,851] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:52:17,851] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:52:17,851] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	80.6905	684	1568	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	80.4079	726	1568	95	below_threshold
Pleomorphomonas diazotrophica	strain=R5-392	GCA_900114935.1	1166257	1166257	type	True	80.2363	648	1568	95	below_threshold
Pleomorphomonas diazotrophica	strain=R5-392	GCA_002844595.1	1166257	1166257	type	True	80.1721	651	1568	95	below_threshold
Pleomorphomonas oryzae	strain=DSM 16300	GCA_000422965.1	261934	261934	type	True	79.8057	610	1568	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	79.3932	654	1568	95	below_threshold
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	78.8048	499	1568	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.8139	269	1568	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.7994	387	1568	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.6071	356	1568	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	77.1494	215	1568	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.9007	327	1568	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:17,852] [INFO] DFAST Taxonomy check result was written to GCF_021864535.1_ASM2186453v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:17,853] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:17,853] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:17,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf286f622-2f74-4e8a-8006-39212aa7d0ce/dqc_reference/checkm_data
[2024-01-25 17:52:17,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:17,900] [INFO] Task started: CheckM
[2024-01-25 17:52:17,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021864535.1_ASM2186453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021864535.1_ASM2186453v1_genomic.fna/checkm_input GCF_021864535.1_ASM2186453v1_genomic.fna/checkm_result
[2024-01-25 17:53:06,783] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:06,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:06,805] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:06,806] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:06,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021864535.1_ASM2186453v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:06,806] [INFO] Task started: Blastn
[2024-01-25 17:53:06,806] [INFO] Running command: blastn -query GCF_021864535.1_ASM2186453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf286f622-2f74-4e8a-8006-39212aa7d0ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_021864535.1_ASM2186453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:08,647] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:08,650] [INFO] Selected 11 target genomes.
[2024-01-25 17:53:08,650] [INFO] Target genome list was writen to GCF_021864535.1_ASM2186453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:08,669] [INFO] Task started: fastANI
[2024-01-25 17:53:08,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg687f3fbb-0903-450d-a213-640eccdec944/GCF_021864535.1_ASM2186453v1_genomic.fna.gz --refList GCF_021864535.1_ASM2186453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021864535.1_ASM2186453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:19,440] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:19,449] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:53:19,449] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000425185.1	s__Pleomorphomonas koreensis	80.6913	685	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	80.3795	730	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_002844595.1	s__Pleomorphomonas diazotrophica	80.17	652	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000422965.1	s__Pleomorphomonas oryzae	79.8339	608	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759535.1	s__Pleomorphomonas sp011759535	79.7318	633	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018262575.1	s__Pleomorphomonas sp018262575	79.472	549	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	79.3925	654	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_004366315.1	s__Pleomorphomonas sp004366315	79.385	512	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262505.1	s__Pleomorphomonas sp018262505	79.3709	585	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839445.1	s__Chthonobacter albigriseus	78.8128	498	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839525.1	s__Mongoliimonas rhizosphaerae	78.7779	516	1568	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:19,450] [INFO] GTDB search result was written to GCF_021864535.1_ASM2186453v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:19,451] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:19,453] [INFO] DFAST_QC result json was written to GCF_021864535.1_ASM2186453v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:19,454] [INFO] DFAST_QC completed!
[2024-01-25 17:53:19,454] [INFO] Total running time: 0h1m29s